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BioC 3.0: CHECK report for MinimumDistance on perceval

This page was generated on 2015-04-10 09:56:57 -0700 (Fri, 10 Apr 2015).

Package 556/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MinimumDistance 1.10.2
Robert B Scharpf
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MinimumDistance
Last Changed Rev: 99352 / Revision: 102249
Last Changed Date: 2015-02-10 18:08:54 -0800 (Tue, 10 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: MinimumDistance
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.10.2.tar.gz
StartedAt: 2015-04-10 03:47:45 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:58:53 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 668.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MinimumDistance.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.10.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MinimumDistance’ version ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .gigignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MinimumDistance’ can be installed ... [42s/52s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [89s/89s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
FilterParamMD 47.523  4.078  51.655
pedigreeGrid  12.111  0.784  12.982
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [123s/128s]
 [124s/129s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BSgenome.Hsapiens.UCSC.hg18’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.

MinimumDistance.Rcheck/00install.out:

* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘colMads’ from package ‘matrixStats’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)

MinimumDistance.Rcheck/MinimumDistance-Ex.timings:

nameusersystemelapsed
DNAcopyParam0.0200.0010.021
FilterParamMD47.523 4.07851.655
MAP20.6420.0280.671
MDRanges-class0.0560.0000.056
MinDistGRanges-class0.1140.0040.118
MinDistGRanges0.0690.0010.072
ParentOffspring-class0.0030.0000.003
ParentOffspringList-class0.0040.0000.005
Pedigree0.0150.0010.016
TrioSet2.7450.1022.895
acf20.0050.0000.005
md_exp0.0020.0010.002
pedigreeGrid12.111 0.78412.982
pedigreeViewports0.0040.0000.005